You'll want to pay due diligence when lining everything up - the big one being pinion angle, but that doesn't mean cut corners anywhere else. Your factory u-bolts should have worn a nice groove in the axle housing by now, so use those as reference for left and right. You'll want to measure anyways to double check, but those ought to be close.
Pinion angle... do some research.
http://www.hotrod.com/articles/91758/ is sort of a "race" article but hey, you're lowering a truck - race away. The information in there is relevant anyways..
"Sometimes corrections need to be made at the front of the vehicle to ensure that the engine and trans are sitting in the proper location. According to Currie, the average car crafter should strive for between 1 and 3 degrees between the tailshaft of the transmission and driveshaft, and 1 to 3 degrees between the driveshaft and pinion. Furthermore, the two angles should be nearly equal (between 1 and 3 degrees), but always opposite."
If you're tech savvy (and I'm donning my fire suit as I type this) - there's an app for that. I've seen David Freiburger use it, so I should be off the hook for bringing it up, right? I've never used it, but here's a link for it:
http://www.superchevy.com/how-to/transmission/1502-how-to-use-tremec-driveline-angle-finder-app/
That link also holds some more insight on pinion angle after the Tremec plug, as well as some good illustrations to help understand the process and why you need to be thorough when setting this angle.
